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Okay, this is less of a theory and more...I don't know, just an idea I got based on Historia/in-game text. So here's how it goes in my mind:

The Great Deku Tree summons Link to halt the curse placed on him by Ganondorf. Link succeeds and takes possession of the Kokiri's Emerald, and the Deku Tree sends him to see Princess Zelda before succumbing to the curse. Standard stuff so far.

When Link goes to see Zelda, however, she has no idea why he's there, and has no doubts about Ganondorf's allegiance to the King of Hyrule. With nothing to go on, Link departs, keeping tabs on Ganondorf at all times, but without Zelda and Impa's help, he never puts into action a plan to open the Door of Time and reach the Triforce.

Years pass, and eventually, Ganondorf and his band of thieves somehow find a way into the Sacred Realm. Ganondorf attempts to claim the Triforce, but it splits into its three components, imbuing Ganondorf with Power, Zelda with Wisdom, and Link with Courage.

Emboldened, Link attempts to stop Ganondorf from conquering Hyrule, but without the aid of the Master Sword or the various trials that made him a hero in the Adult Timeline, Link is defeated. Ganondorf claims the last two pieces of the Triforce, transforming into the Demon King Ganon. The ancient sages (not the ones from OoT, possibly those seen in Twilight Princess) seal Ganon away in the Sacred Realm, temporarily defeating him.

However, Ganon and his armies eventually break free, leading to the Imprisoning War as described in the backstory of LttP. Through all the carnage, Zelda desperately thinks of a plan to make things right. By her divine power, she prays for the entire crisis to be averted, to have Ganondorf punished before he can rise to power. Unfortunately, she is unable to change her own timeline, but her prayers are indeed answered.

Years earlier, a young Zelda has a dream in which dark storm clouds billow over the land of Hyrule until the darkness is dispelled by a figure from the forest holding a green and shining stone, followed by a fairy...

I believe in infinite timelines, but only from feasible possibilities. Everything checks out except the only way I can see Ganondorf avoiding tipping off Zelda's spidey sense is that she never got to see him. Something happened differently (like she got a cold and was in her chambers) that made it so she never saw Ganondorf, never realized the threat because she never saw his "evil eyes" and began to doubt him.

Just for anyone who doesn't know about the timeline (officially released by Nintendo). That aside, this theory makes perfect sense. It's honestly the only time I've seen someone go in-depth of this particular branch of the timeline. It's extremely well done.

Oh, you're completely not a dick haha. I don't have the exact wording handy, but I think the LttP backstory has Ganondorf's thieves find a hidden way into the Sacred Realm, so I just went with "he somehow got around it."

I don't think that the 3 stones were required to enter the sacred realm when it was created. They're needed in OoT, yes, but in TP, when you go through the time portal and arrive in the past version of the Temple of Time, there is no alter for the three stones, so in that sense, it would seem that the gods had eventually tried to add additional "security" to the sacred realm by requiring those three stones. Considering how in TP, there is a stair case of light that leads into a dungeon, it might be true that there are other ways in and out of that dungeon which connects to the sacred realm without the need to open the Door of Time.

Remember that TP takes place after OoT. Link opened the way to the Sacred Realm when he used the Stones. Ganondorf broke in as a direct result. The Godesses apparently ditched the use of the Stones in TP.

I find it strange that in OoT, opening the Door of The Temple provides a path to the future; but in TP, doing so flashes you back to the past.

This is an interesting theory, but the Historia says the timeline split occurs in the final battle with Ganondorf. If you notice, it outlines all the events of OoT, right up to Ganondorf kidnapping Zelda. The next section is titled the "Decisive Battle with Ganondorf." There's a little box saying that if the hero loses, the defeated hero timeline begins.

However, aside from its arbitrariness, I still think the defeated hero timeline is problematic. The biggest problem is that the Triforce is purportedly a source of limitless power. You spend most of your time in all of the games trying to prevent Ganon from obtaining the completed Triforce. However, the defeated hero timeline basically implies that even with the omnipotent Triforce, Ganon could be overwhelmed and defeated---without the hero, nonetheless! This timeline undermines both the power of Triforce and value of Link as the hero.

Ah...well...juuust gonna ignore that detail. :P For real though, thanks for pointing that out; I'll just settle for head canon for now haha.

I agree with your second point, but then, he did manage to do more damage in the war than in any of the games...still though. That backstory's just a relic from when the Triforce wasn't completely omnipotent, I guess.

Yeh, I could've been a bit clearer, I guess. This little write-up (theory, fanfic, whatev) proposes Zelda's prophetic dream you hear about that warns her about Ganondorf is a result of her prayer I described here. I'll edit the post when I get home!

The title states Timeline Theory. A recurring theme in The Legend of Zelda, is Timetravel. And with any timetravel comes the possibility of creating alternate timelines. The whole point of the post is that it is a theory, which means it's not neccessarily fact. What I think /u/dahahawgy is trying to explain is that this was the original timeline, where Zelda didn't know of Ganondorf's intention, and all this happened, which then led to the events that started Ocarina of Time.